Discovery of novel metabolites in Colombian specialty coffee via multiplatform untargeted metabolomics during...

The metabolite composition of Arabica coffee during solid-state fermentation remains insufficiently characterized. This study examined changes in mucilage and endosperm metabolites on a Colombian smallholder farm using gas and liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (GC-QTOF-MS and LC-QTOF-MS). Across three batches, more than 600 compounds were detected in both matrices. Samples were collected at 0, 5 and 10 h, with depth-resolved sampling in one batch. Among 63 GC-QTOF-MS library-identified compounds, 42 discriminated between endosperm and mucilage, while 11 and 2 differentiated fermentation time in mucilage and endosperm, respectively. From 557 LC-QTOF-MS(+) features, 206 were discriminant and annotated at varying confidence levels. More discriminant metabolites were found in mucilage than in endosperm, although endosperm showed the highest number at the end of fermentation. In total, 269 compounds were identified, including 193 newly reported in coffee fermentation. The findings highlight distinct metabolite fingerprints, and novel metabolites of potential importance.